The heater won't decrease FE. It works by running engine coolant through the heater core, which is basically a small radiator inside the car's climate control system. Of course this also means that the heater won't work until the engine warms up. If the heater wasn't on, the radiator would get rid of the excess heat anyway.
Auto climate control won't make much difference compared to normal AC. Actually, if you could manage the car's temperature as well as auto climate control does, there would probably be no difference. All auto AC really does is turn the knobs for you. The rest of the system is the same. The one thing auto AC will do that could decrease fuel economy compared to normal AC is that it will operate at maximum power when you get into a hot car and turn it on. Of course you can do this in a car with normal AC as well. Just set it to max until the car gets cooled off, then adjust it to a normal setting.
Auto climate control won't use the AC if the outside air is cool enough. Instead it will just draw cool air from outside. Thus if you have the temperature set for 25C in 10C weather, decide you're too warm, and lower it to 22C, it will just use the cool outside air to adjust the cabin temperature instead of the AC. I'm not sure about the heater. Since waste heat is essentially free, I don't care if the car uses the heater or not so I've never worried about the reverse of this situation.
You don't have to turn off auto climate control to turn off AC. A lot of auto climate control systems have an AC button separate from the main auto climate on/off button. The ones that don't (Ford, at least in the US) have mode selection buttons, and only the full auto, AC (may be 2 AC modes), and possibly defog/defrost settings will use the AC. Other modes allow the car to use heat and outside air as needed. Some cars will the AC and heater at the same time in defog mode. AC also removes moisture from the air, and warm, dry air works best for defogging the windshield. If your car does this, you can also use it to dry out the cabin on cold, rainy days.
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